Catholic Archbishop Thomas Wenski and the Miami archdiocese have sued the City of Miami for $89 million, claiming its Miami 21 zoning code devalued church property occupied by LaSalle High School and the Shrine to our Lady of Charity in Coconut Grove.

The lawsuit, filed last week in Miami-Dade circuit court, also asks a judge to annul sections of the code, approved in 2009, that according to Wenski and archdiocese lawyers bar construction of structures taller than two stories on its four properties, which sit just south of the Vizcaya Museum and Gardens and were once part of that estate.

The suit was filed under a controversial state law, the Bert J. Harris Act, that was designed to allow owners of property to claim compensation when government decisions significantly reduce its value. Experts say no Harris act claim has ever been won in court, in part because the law is vague and untested, although cases are often settled.

City officials said the suit has no merit.

The archdiocese first filed a Harris claim with the city three years ago, alleging a $139 million loss in value. An archdiocese spokeswoman said the suit was filed because city officials did not respond to the claim or meet with church representatives — an allegation city officials deny. The spokeswoman did not explain the difference in the dollar amounts claimed.

Archdiocese spokeswoman Mary Ross Agosta called the Miami 21 zoning rules for the area, crafted in part to protect the historic Vizcaya’s “view corridors’’ from intrusion by high-rise structures, “unfair.’’

“It could affect whatever future ministries we need to put in those areas, limit us to height, possibly location on the property, and really interfere with our mission,’’ she said.

The archdiocese, which pays no taxes on its properties because it’s exempt as a religious institution, currently has no plans to redevelop or sell the sites, she said. The properties also include a youth center and an assisted-living facility. The controversy has spurred speculation that the Archdiocese is considering selling the Shrine of our Lady of Charity. Ross dismissed those rumors.

“Absolutely not,’’ she said. “We would never, ever, ever, ever sell the property or the Shrine of our Lady of Charity.’’

The properties in question do not include the adjacent Mercy Hospital site, which has separate ownership. A waterfront hospital parking lot has been at the center of ongoing high-profile legal battles over a proposed high-rise condo development that would have been visible from Vizcaya. Courts overturned the city approval of the planned towers.

Miami Mayor Tomas Regalado said he was surprised by the archdiocese claim because he believes the Mercy court decisions settled the legal question over the propriety of height restrictions near Vizcaya.

“I thought that was a closed chapter,’’ Regalado said.

Miami City Attorney Julie Bru did not respond to requests for comment.

But some legal experts say that, without a specific plan to redevelop or sell the property for redevelopment, the archdiocese can’t claim the value of its properties has been reduced.

“You have to have taken some step, presented some plan for a project,’’ said Miami Commission Chairman Marc Sarnoff, a lawyer whose district includes the archdiocese properties. “You can’t speculate and say your rights have been violated.’’

One top expert on the Harrris Act who is not involved in the case agrees.

Richard Ovelmen, an attorney who has litigated Harris Act cases and has written scholarly articles on the law, said the archdiocese suit, which he has read, doesn’t appear to meet two critical tests. The act bars claims of loss based on mere speculative analysis, and requires that the property owner have made an investment in the land with the expectation of making a return on that investment, he said.

The archdiocese obtained the land decades ago from the heirs of Vizcaya builder James Deering to build a school, hospital and other charitable facilities.

“It doesn’t seem to me there would be a violation here because the archdiocese claim is speculative,’’ said Ovelmen, a partner at Jorden Burt. “Nor does Miami 21 seem to thwart any reasonable investment-backed expectations. It just doesn’t seem the archdiocese made any investment in the land with that purpose.’’

Partners in the law firm that filed the lawsuit on behalf of the archdiocese, Bilzin Sumberg Baena Price & Axelrod, have been longstanging critics of Miami 21, a new set of pedestrian-friendly zoning rules designed to protect neighborhoods from intrusive development. Partners Carter McDowell and Vicky Garcia-Toledo helped lead an unsuccessful public charge against the new code — which they claimed would reduce property values and bring development in Miami to standstill — while it was under consideration.

An appraiser hired by the archdiocese based the $89 million estimate of the loss in property value by calculating the difference between what the “highest and best’’ use of the properties would have been under the previous zoning code — that is, if they were to be fully redeveloped with residential and other permitted uses — and what’s allowed under Miami 21.

The new zoning rules do not limit uses of the property beyond those in the old zoning code, but do impose height and density restrictions and other rules on how new buildings could be designed in the future.

The suit claims the rules effectively limit new construction on archdiocese properties to two stories, in part to make development on the site compatible with abutting single-family neighborhoods. It also claims Miami 21 singled out the church properties for strict height limits — the view corridor rules — that apply nowhere else in the city. It also contends that the old code had no height limits for those properties.

But architect and planner Elizabeth Plater-Zyberk, the lead consultant on Miami 21, said that’s an unrealistically strict reading of the code. Plater-Zyberk said she met with archdiocese officials to explain that Miami 21 rules allow special plans with substantial flexibility for large parcels.

“I suggested to them that they should present a plan to determine what’s possible,’’ she said.

Sarnoff said he and other city officials also met with archdiocese representatives.

“I’ve seen plans where they could build up to 15 stories in some areas,’’ Sarnoff said. “But in the suit, they seem to say they wre unaware of that possibility.’’